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Update Swissprot database

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This commit is contained in:
Eric Coissac
2025-05-22 02:23:26 +02:00
parent 4b71fe8c4c
commit 3589bf03eb
374 changed files with 28354 additions and 160 deletions
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47
detectors/cds/tools/build_swissprot_db.sh
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@ -22,8 +22,8 @@ CORE_GENES="$CORE_GENES infA"
CORE_GENES="$CORE_GENES matK"
CORE_GENES="$CORE_GENES ndhA ndhB ndhC ndhD ndhE ndhF ndhG ndhH ndhI ndhJ ndhK"
CORE_GENES="$CORE_GENES petA petB petD petG petL petN"
CORE_GENES="$CORE_GENES psaA psaB psaC psaI psaJ psbA"
CORE_GENES="$CORE_GENES psbB psbC psbD psbE psbF psbH psbI psbJ psbK psbL psbM psbN psbT psbZ"
CORE_GENES="$CORE_GENES psaA psaB psaC psaI psaJ"
CORE_GENES="$CORE_GENES psbA psbB psbC psbD psbE psbF psbH psbI psbJ psbK psbL psbM psbN psbT psbZ"
CORE_GENES="$CORE_GENES rbcL"
CORE_GENES="$CORE_GENES rpl14 rpl16 rpl2 rpl20 rpl22 rpl23 rpl32 rpl33 rpl36"
CORE_GENES="$CORE_GENES rpoA rpoB rpoC1 rpoC2"
@ -297,7 +297,7 @@ function dereplicate_genes() {
function buildGeneBlastDB() {
local gene="${1}"
local fastain="${gene}/${gene}.cdhit.fst"
local fastain="${gene}/${gene}.fst"
loginfo " formatting Blast $gene DB"
timeoutcmd 300 makeblastdb -dbtype prot -in ${fastain} >& /dev/null
@ -313,7 +313,7 @@ function buildBlastDBs() {
}
function list_shell_genes() {
pushd $SPDIR
pushd $SPDIR 1>&2
ls genes \
| grep -v '\.' \
@ -321,7 +321,7 @@ function list_shell_genes() {
| grep -iv '^orf' \
| grep -iv "$RPS12_GENE"
popd
popd 1>&2
}
function list_dust_genes() {
@ -342,10 +342,10 @@ function build_core_libraries() {
mkdir -p core
for gene in $CORE_GENES ; do
cp genes/$gene/$gene.cdhit.fst core/$gene.fst
cp genes/$gene/$gene.cdhit.fst.phr core/$gene.fst.phr
cp genes/$gene/$gene.cdhit.fst.pin core/$gene.fst.pin
cp genes/$gene/$gene.cdhit.fst.psq core/$gene.fst.psq
cp genes/$gene/$gene.fst core/$gene.fst
cp genes/$gene/$gene.fst.phr core/$gene.fst.phr
cp genes/$gene/$gene.fst.pin core/$gene.fst.pin
cp genes/$gene/$gene.fst.psq core/$gene.fst.psq
done
popd 1>&2
@ -359,10 +359,10 @@ function build_rps12_library() {
rm -rf RPS12
mkdir -p RPS12
cp genes/$gene/$gene.cdhit.fst RPS12/$gene.fst
cp genes/$gene/$gene.cdhit.fst.phr RPS12/$gene.fst.phr
cp genes/$gene/$gene.cdhit.fst.pin RPS12/$gene.fst.pin
cp genes/$gene/$gene.cdhit.fst.psq RPS12/$gene.fst.psq
cp genes/$gene/$gene.fst RPS12/$gene.fst
cp genes/$gene/$gene.fst.phr RPS12/$gene.fst.phr
cp genes/$gene/$gene.fst.pin RPS12/$gene.fst.pin
cp genes/$gene/$gene.fst.psq RPS12/$gene.fst.psq
popd 1>&2
}
@ -373,11 +373,12 @@ function build_shell_libraries() {
rm -rf shell
mkdir -p shell
for gene in $(list_shell_genes) ; do
cp genes/$gene/$gene.cdhit.fst shell/$gene.fst
cp genes/$gene/$gene.cdhit.fst.phr shell/$gene.fst.phr
cp genes/$gene/$gene.cdhit.fst.pin shell/$gene.fst.pin
cp genes/$gene/$gene.cdhit.fst.psq shell/$gene.fst.psq
for gene in $(list_shell_genes) ; do
echo installing shell gene $gene into shell library... 1>&2
cp genes/$gene/$gene.fst shell/$gene.fst
cp genes/$gene/$gene.fst.phr shell/$gene.fst.phr
cp genes/$gene/$gene.fst.pin shell/$gene.fst.pin
cp genes/$gene/$gene.fst.psq shell/$gene.fst.psq
done
popd 1>&2
@ -390,10 +391,10 @@ function build_dust_libraries() {
mkdir -p dust
for gene in $(list_dust_genes) ; do
cp genes/$gene/$gene.cdhit.fst dust/$gene.fst
cp genes/$gene/$gene.cdhit.fst.phr dust/$gene.fst.phr
cp genes/$gene/$gene.cdhit.fst.pin dust/$gene.fst.pin
cp genes/$gene/$gene.cdhit.fst.psq dust/$gene.fst.psq
cp genes/$gene/$gene.fst dust/$gene.fst
cp genes/$gene/$gene.fst.phr dust/$gene.fst.phr
cp genes/$gene/$gene.fst.pin dust/$gene.fst.pin
cp genes/$gene/$gene.fst.psq dust/$gene.fst.psq
done
popd 1>&2
@ -482,7 +483,7 @@ mkdir -p rawdata
pushd rawdata
download_swissprot | extract_chloro_entries > SP_Chloro.dat
download_swissprot | gzip -dc | extract_chloro_entries > SP_Chloro.dat
extract_fasta_protein SP_Chloro.dat > SP_Chloro_gene_db.fst